cirrocumulus

cirrocumulus copied to clipboard

Cirrocumulus

Cirrocumulus is an interactive visualization tool for large-scale single-cell genomics data, with the following features:

• Visualize datasets in h5ad_, 10x h5, Xenium, loom_, Seurat_, TileDB_, or zarr_ formats
• View MERFISH_ or other spatial transcriptomics data overlaid on an image
• Easily deploy on a laptop, on-premise server, cloud VM, or Google App Engine
• Share the current visualization state in a URL
• Share datasets securely with collaborators
• Create dotplots, heatmaps, and violin plots to explore relationships between categorical variables and expression
• Generate composition plots to inspect cluster makeup
• Explore complete differential expression results generated by Scanpy_ or Pegasus/Cumulus
• Interactively create and share “AND” or “OR” filters
• Collaboratively annotate cell types in real time, optionally using a controlled vocabulary (example ontology_)
• Quickly load multiple features from predefined lists (see example_)
• Explore multiple features and embeddings simultaneously
• Fast interactive exploration of 2 and 3-d embeddings of millions of cells, including zoom, pan, rotate (3-d), and lasso tools
• Save publication quality images
• Highly customizable - for example, set the color map, point size, or whether to use fog for 3-d embeddings to fade distant points

Quick Start

Install the package::

pip install cirrocumulus

Launch cirrocumulus via the command line::

cirro launch <path_to_dataset>

• Launch accepts more than one dataset to enable quick dataset switching or to combine modalities (e.g gene fusions and expression) stored in separate files.

Example Data ^^^^^^^^^^^^^

• Download 3k PBMCs from a healthy donor data_ and launch::

  cirro launch pbmc3k.h5ad --markers markers.json

• Download human lymph node spatial data_ and launch::

  cirro launch V1_Human_Lymph_Node/V1_Human_Lymph_Node.h5ad --spatial V1_Human_Lymph_Node/spatial

.. image:: images/play3d.gif

Complete documentation available at https://cirrocumulus.readthedocs.io

.. _3k PBMCs from a healthy donor data: https://github.com/klarman-cell-observatory/cirrocumulus/raw/master/docs/pbmc3k.zip .. _human lymph node spatial data: https://github.com/klarman-cell-observatory/cirrocumulus/raw/master/docs/V1_Human_Lymph_Node.zip .. _h5ad: https://anndata.readthedocs.io/ .. _loom: https://linnarssonlab.org/loompy/format/ .. _STAR-Fusion: https://github.com/STAR-Fusion/STAR-Fusion/wiki .. _Seurat: https://satijalab.org/seurat/ .. _see example: https://github.com/klarman-cell-observatory/cirrocumulus/raw/master/docs/markers.json .. _Pegasus: http://pegasus.readthedocs.io/ .. _Cumulus: https://cumulus.readthedocs.io/en/stable/cumulus.html .. _Scanpy: https://scanpy.readthedocs.io/ .. _TileDB: https://tiledb.com/ .. _zarr: https://zarr.readthedocs.io/ .. _example ontology: http://www.obofoundry.org/ontology/cl.html .. _10x h5: https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/advanced/h5_matrices .. _MERFISH: https://www.biorxiv.org/content/10.1101/2023.03.06.531121v1 .. _Xenium: https://www.10xgenomics.com/support/in-situ-gene-expression/documentation/steps/onboard-analysis/at-a-glance-xenium-output-files